Exclude files staged as deleted fom `git ls-files`

I use git ls-files in a script to collect all files tracked by git. Unfortunately if you rm a file (rather than git rm) it does not exist on the file system any more but it will still be listed by git ls-files

So the question: Is there a simple and efficient way to exclude files which do not exist on file system any more from either the git ls-files output itself or by filtering it afterwards (using e.g. bash)? Something like

git ls-files --existing-only

Background: I want to create a CMake dummy target, which holds all files that are part of the project directory (i.e. tracked by git). And I use something like

execute_process(
    COMMAND bash -c "cd ${CMAKE_SOURCE_DIR}; git ls-files"
    OUTPUT_VARIABLE ADDITIONAL_PROJECT_FILES
)

to generate the file list. But unfortunately rming a file and not yet staging the change will result in errors because the file can't be found by CMake any more..

Update: Before my edit I was talking about git rming a file - which will be handled correctly by git ls-files. But the problem persists: If someone removes a file (without using git for it) git ls-files will list it (and I run into trouble).

comm -23 <(git ls-files | sort) <(git ls-files --deleted | sort)

From comm --help:

  -2              suppress column 2 (lines unique to FILE2)
  -3              suppress column 3 (lines that appear in both files)